17 papers · ranked by Valyu relevance
Florian Teichert, Ugo Bastolla, Markus Porto
Background The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of protein structures. Therefore, instead of manipulating coordinates directly, matrices of inter-atomic distances, sets of vectors between protein…
Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma R Chandra
Background Design of protein structure comparison algorithm is an important research issue, having far reaching implications. In this article, we describe a protein structure comparison scheme, which is capable of detecting correct alignments even in difficult cases, e.g. non-topological similarities. The proposed…
Bjoern Kolbeck, Patrick May, Tobias Schmidt-Goenner, Thomas Steinke + 1 more
'Ernst-Walter Knapp'] Background Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of…
Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann + 2 more
'Alexandre G. de Brevern' 'Narayanaswamy Srinivasan'] Protein structure alignment is a crucial step in protein structure-function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These…
Gabriele Mayr, Francisco S Domingues, Peter Lackner
Background Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by…
Roberto Mosca, Barbara Brannetti, Thomas R Schneider
Background Structural alignment is an important step in protein comparison. Well-established methods exist for solving this problem under the assumption that the structures under comparison are considered as rigid bodies. However, proteins are flexible entities often undergoing movements that alter the positions of…
Che-Lun Hung, Yaw-Ling Lin
Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the…
Jianbo Lu, Guoliang Xu, Shihua Zhang, Benzhuo Lu
Background Superpositioning is an important problem in structural biology. Determining an optimal superposition requires a one-to-one correspondence between the atoms of two proteins structures. However, in practice, some atoms are missing from their original structures. Current superposition implementations address…
Ashar J Malik, Siying Mao, Philip Hugenholtz, David B Ascher + 1 more
Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-based approaches. Encoding three-dimensional protein structures using a simplified structure-aware alphabet can lead to compact, comparable strings that retain key spatial…
Shweta B. Shah, Nikolaos V. Sahinidis, Vasilis J. Promponas
Protein structure alignment is the problem of determining an assignment between the amino-acid residues of two given proteins in a way that maximizes a measure of similarity between the two superimposed protein structures. By identifying geometric similarities, structure alignment algorithms provide critical insights…
Ping Ge, Shaojie Zhang
The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align…
Zaixin Lu, Zhiyu Zhao, Bin Fu
Background Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are very helpful for protein biologists. However, an accurate alignment algorithm itself may be…
Changhoon Kim, Jodi Basner, Byungkook Lee
Background Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins…
René Staritzbichler, Edoardo Sarti, Emily Yaklich, Antoniya Aleksandrova + 4 more
'Antoniya Aleksandrova' 'Marcus Stamm' 'Kamil Khafizov' 'Lucy R. Forrest' 'Frederique Lisacek'] The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge…
R C Marinescu Tanasoca, L Angibaud, N Kort, F Billi + 7 more
'J Eberhardt' 'E Franceschetti' 'D Jeremic' 'A Klasan' 'P A Vendittoli' 'G M Avram'] 1. The main goal of a successful total knee arthroplasty is to relieve pain and restore function. While mechanical alignment provides excellent long-term implant survivorship, clinical and functional outcomes remain less than ideal. 2.…
Simon Talbot, Pandelis Dimitriou, Michael Mullen, John Bartlett
Purpose Firstly, to assess and compare the accuracy and reproducibility of the sulcus line compared to Whiteside’s line. Secondly, to assess the accuracy of intraoperative techniques for using the rotational alignment of the trochlear groove to set femoral rotation. Thirdly, to assess the reproducibility of a trochlear…
Byung Woo Cho, Tae-Ho Lee, Sungjun Kim, Chong-Hyuk Choi + 3 more
'Koo Yeon Lee' 'Sung-Hwan Kim'] This study aimed to analyze the reproducibility and reliability of the alignment parameters measured using the EOS image system in both limbs while standing with an even weight-bearing posture. Overall, 104 lower extremities in 52 patients were analyzed retrospectively. The patients…